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comparison qiime2-2020.8/qiime_vsearch_uchime-denovo.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_vsearch_uchime-denovo" name="qiime vsearch uchime-denovo"
3 version="2020.8">
4 <description>De novo chimera filtering with vsearch.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime vsearch uchime-denovo
10
11 --i-sequences=$isequences
12
13 --i-table=$itable
14
15 --p-dn=$pdn
16
17 --p-mindiffs=$pmindiffs
18
19 --p-mindiv=$pmindiv
20
21 --p-minh=$pminh
22
23 --p-xn=$pxn
24
25 --o-chimeras=ochimeras
26
27 --o-nonchimeras=ononchimeras
28
29 --o-stats=ostats
30
31 #if str($examples) != 'None':
32 --examples=$examples
33 #end if
34
35 ;
36 cp ostats.qza $ostats
37
38 ]]></command>
39 <inputs>
40 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data" />
41 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table (used for computing total feature abundances). [required]" name="itable" optional="False" type="data" />
42 <param label="--p-dn: NUMBER No vote pseudo-count, corresponding to the Range(0.0, None) parameter n in the chimera scoring function. [default: 1.4]" min="0.0" name="pdn" optional="True" type="float" value="1.4" />
43 <param label="--p-mindiffs: INTEGER Minimum number of differences per segment. Range(1, None) [default: 3]" min="1" name="pmindiffs" optional="True" type="integer" value="3" />
44 <param label="--p-mindiv: NUMBER Minimum divergence from closest parent. Range(0.0, None) [default: 0.8]" min="0.0" name="pmindiv" optional="True" type="float" value="0.8" />
45 <param exclude_max="False" label="--p-minh: PROPORTION Range(0.0, 1.0, inclusive_end=True) Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]" max="1.0" min="0.0" name="pminh" optional="True" type="float" value="0.28" />
46 <param exclude_min="True" label="--p-xn: NUMBER Range(1.0, None, inclusive_start=False) No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]" max="None" min="1.0" name="pxn" optional="True" type="float" value="8.0" />
47 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
48
49 </inputs>
50
51 <outputs>
52 <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras" />
53 <data format="qza" label="${tool.name} on ${on_string}: nonchimeras.qza" name="ononchimeras" />
54 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats" />
55
56 </outputs>
57
58 <help><![CDATA[
59 De novo chimera filtering with vsearch.
60 ###############################################################
61
62 Apply the vsearch uchime_denovo method to identify chimeric feature
63 sequences. The results of this method can be used to filter chimeric
64 features from the corresponding feature table. For additional details,
65 please refer to the vsearch documentation.
66
67 Parameters
68 ----------
69 sequences : FeatureData[Sequence]
70 The feature sequences to be chimera-checked.
71 table : FeatureTable[Frequency]
72 Feature table (used for computing total feature abundances).
73 dn : Float % Range(0.0, None), optional
74 No vote pseudo-count, corresponding to the parameter n in the chimera
75 scoring function.
76 mindiffs : Int % Range(1, None), optional
77 Minimum number of differences per segment.
78 mindiv : Float % Range(0.0, None), optional
79 Minimum divergence from closest parent.
80 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
81 Minimum score (h). Increasing this value tends to reduce the number of
82 false positives and to decrease sensitivity.
83 xn : Float % Range(1.0, None, inclusive_start=False), optional
84 No vote weight, corresponding to the parameter beta in the scoring
85 function.
86
87 Returns
88 -------
89 chimeras : FeatureData[Sequence]
90 The chimeric sequences.
91 nonchimeras : FeatureData[Sequence]
92 The non-chimeric sequences.
93 stats : UchimeStats
94 Summary statistics from chimera checking.
95 ]]></help>
96 <macros>
97 <import>qiime_citation.xml</import>
98 </macros>
99 <expand macro="qiime_citation"/>
100 </tool>